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awk to compare each file in two directores by storing in variable

 
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Old 09-30-2016
awk to compare each file in two directores by storing in variable
In the below bash I am trying to read each file from a specific directory into a variable REF or VAL. Then use those variables in an awk to compare each matching file from REF and VAL. The filenames in the REF are different then in the VAL, but have a common id up until the _ I know the awk portion works as I can run files through them manually. However, I am not sure if I am doing the variable part correctly. Thank you Smilie.

The two variables are:

REF comes from /home/cmccabe/Desktop/comparison/reference/10bp and is 3 files:

Code:
 S1234_ref.txt
 A5678_ref.txt
 T1111_ref.txt

VAR comes from /home/cmccabe/Desktop/comparison/validation/files
 and is 3 files:

Code:
 S1234_panel.vcf
 A5678_panel.vcf
 T1111_panel.vcf

So, S1234_ref.txt would be REF and S1234_panel.vcf would be VAL, then those two files would be compared. I think I am close but not too sure about the variables.

Code:
 REF=/home/cmccabe/Desktop/comparison/reference/10bp
VAL=/home/cmccabe/Desktop/comparison/validation/files
awk -F'\t' -v OFS='\t' 'FNR==1 { next }
      FNR == NR { file1[$2,$4,$5] = $2 FS $4 FS $5 }
      FNR != NR { file2[$2,$4,$5] = $2 FS $4 FS $5 }
            END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
            print "Missing in Reference but found in IDP:"; for (k in file2) if (!(k in file1)) print file2[k]
            print "Missing in IDP but found in Reference:"; for (k in file1) if (!(k in file2)) print file1[k]
      }'$REF $VAL > /home/cmccabe/Desktop/comparison/ref_val/concordance.txt

Last edited by cmccabe; 09-30-2016 at 04:01 PM.. Reason: added details
 
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